/ubuntu

Setting-up scripts for Ubuntu 18.04

Primary LanguageShellMIT LicenseMIT

Setting-up scripts for Ubuntu 18.04

The whole developing environment is based on Linuxbrew. Many of the following steps also works under macOS via Homebrew.

Linux specific scripts were placed in prepare/. This repo contains macOS related codes.

Install packages needed by Linuxbrew and some others

echo "==> When some packages went wrong, check http://mirrors.ustc.edu.cn/ubuntu/ for updating status."
bash -c "$(curl -fsSL https://raw.githubusercontent.com/wang-q/ubuntu/master/prepare/1-apt.sh)"

Optional: adjusting Desktop

In GUI desktop, disable auto updates: Software & updates -> Updates, set Automatically check for updates: to Never, untick all checkboxes, click close and click close again.

# Removes nautilus bookmarks and disables lock screen
echo '==> `Ctrl+Alt+T` to start a GUI terminal'
bash -c "$(curl -fsSL https://raw.githubusercontent.com/wang-q/ubuntu/master/prepare/2-gnome.sh)"

Install Linuxbrew

echo "==> Install linuxbrew, copy the next *ONE* line to terminal"
bash -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"

test -d ~/.linuxbrew && PATH="$HOME/.linuxbrew/bin:$HOME/.linuxbrew/sbin:$PATH"
test -d /home/linuxbrew/.linuxbrew && PATH="/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:$PATH"

if grep -q -i linuxbrew $HOME/.bashrc; then
    echo "==> .bashrc already contains linuxbrew"
else
    echo "==> Update .bashrc"

    echo >> $HOME/.bashrc
    echo '# Linuxbrew' >> $HOME/.bashrc
    echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >> $HOME/.bashrc
    echo "export MANPATH='$(brew --prefix)/share/man'":'"$MANPATH"' >> $HOME/.bashrc
    echo "export INFOPATH='$(brew --prefix)/share/info'":'"$INFOPATH"' >> $HOME/.bashrc
    echo "export HOMEBREW_NO_ANALYTICS=1" >> $HOME/.bashrc
    echo "export HOMEBREW_NO_AUTO_UPDATE=1" >> $HOME/.bashrc
    echo >> $HOME/.bashrc
fi

source $HOME/.bashrc

Download

Fill $HOME/bin, $HOME/share and $HOME/Scripts.

bash -c "$(curl -fsSL https://raw.githubusercontent.com/wang-q/dotfiles/master/download.sh)"
source $HOME/.bashrc

Install packages managed by Linuxbrew

Packages includes:

  • Programming languages: Perl, Python, R, Java, Lua and Node.js
  • Some generalized tools
bash $HOME/Scripts/dotfiles/brew.sh
source $HOME/.bashrc

Attentions:

  • There is a post-install step when installing perl, cpan -i XML::Parser. If the process stalled there, just kill the cpan process.

    • Test::RequiresInternet wants to connect to google.com while it was blocked.

  • r and gnuplot have a lot of dependencies, many of which is from linuxbrew/xorg. Just be patient.

  • Sometimes there are no binary packages in https://linuxbrew.bintray.com/bottles/, compiling from source codes may takes extra time.

Packages of each languages

bash $HOME/Scripts/dotfiles/perl/install.sh

bash $HOME/Scripts/dotfiles/python/install.sh

bash $HOME/Scripts/dotfiles/r/install.sh

Bioinformatics Apps

bash $HOME/Scripts/dotfiles/genomics.sh

bash $HOME/Scripts/dotfiles/ensembl.sh

# Optional: huge apps 
# bash $HOME/Scripts/dotfiles/others.sh

MySQL

bash $HOME/Scripts/dotfiles/mysql.sh

# Following the prompts, create mysql users and install DBD::mysql

Optional: dotfiles

bash $HOME/Scripts/dotfiles/install.sh
source $HOME/.bashrc

git clone https://github.com/VundleVim/Vundle.vim.git ~/.vim/bundle/Vundle.vim
vim +PluginInstall +qall

Edit .gitconfig to your own manually.

Directory Organization